The United States is facing increasing difficulty acquiring intelligence needed to run its stealth drone program in Yemen, undermining a campaign against the most lethal branch of al-Qaida after Houthi rebels seized control of parts of the country's security apparatus, U.S. officials say.

Gaps in on-the-ground intelligence could slow America's fight against a resurgent al-Qaida in Yemen and heighten the risk of errant strikes that kill the wrong people and stoke anti-U.S. sentiment, potentially making the militants even stronger in areas where al-Qaida is already growing.

Iran-backed Houthi rebels have taken up positions in and around several defense and intelligence installations whose teams had previously cooperated with Washington, cutting off key sources of information for drone-missile attacks, the officials told Reuters.

Turmoil in the wake of last week's collapse of a U.S.-backed Yemeni government after days of clashes in the capital Sanaa, has already forced the U.S. State Department to reduce staff and operations at the U.S. Embassy.

U.S. officials told Reuters last week that Washington has also halted some counterterrorism operations, but described the measures as temporary.

The turmoil has also cast doubt over the future of a key partnership for Washington in the fight against al-Qaida in the Arabian Peninsula, AQAP. Only last September President Barack Obama touted cooperation with Yemen as a model in counterterrorism.

AQAP claimed responsibility for shootings this month in Paris that killed 17 people and has been accused of plotting attacks against American interests.

The crisis in the Arab world's poorest country threatens to create a power vacuum that could allow AQAP to expand, while pushing Yemen toward a broader conflict between majority Sunni Muslims and minority Shi'ite Houthis, who are hostile to both the United States and al-Qaida.

U.S. officials said training of Yemeni special forces had ground to a halt in the capital, though some joint activities were continuing in the Sunni-controlled south.

Many U.S. personnel remain in place with Yemeni government forces at the southern al-Anaad air base, an intelligence post for monitoring the al-Qaida group.

Stephen Seche, who served as U.S. ambassador to Yemen from 2007 to 2010 and now works in Washington at a law firm, said, however, he expected collaboration between U.S. and Yemeni intelligence services to suffer.

“If there's no leadership, there's no clear direction, there's no real motivation to do that,” he said.

“Collateral damage”

The White House and the Pentagon have said counterterrorism efforts in Yemen will be undeterred by turmoil in the country.

“We do continue to have an ongoing security relationship with the national security infrastructure in Yemen. Some of which, much of which, is still functioning,” White House spokesman Josh Earnest told reporters.

Some U.S. officials, however, privately say the reduced intelligence sharing could undermine the armed drone program.

Information has dried up from Yemeni security offices in Sanaa and there has been less cooperation from local security services outside the capital, the officials told Reuters, speaking on condition of anonymity.

Houthis have erected checkpoints at entrances at security institutions and have stationed operatives inside, Yemeni officials say. Rebels also surround the homes of the defense minister and the head of the National Security Bureau.

U.S. authorities treat some Yemeni intelligence leads with skepticism, concerned local officials might be trying to settle scores, and typically seek corroboration from multiple sources, the officials said.

But they will now be forced to rely more on surveillance drones, spy satellites and electronic eavesdropping, as well as their own “human intelligence” sources on the ground, said one official with direct knowledge of the operations.

With little or no prospects of working with the Houthis, Washington will also face trouble mounting raids on al-Qaida hideouts similar to those carried out in the past by U.S.-trained Yemeni special forces working close with U.S. officials.

The United States will maintain some security cooperation in southern Yemen, an al-Qaida stronghold and where former president Abd-Rabbu Mansour Hadi retains some support, even while the rebels control the capital and much of the north, the officials said.

The U.S. officials added that they can continue drone strikes such as Monday's attack on a car in eastern Yemen that killed three men believed to be al-Qaida militants, including one identified as a youth by a Yemeni rights group.

The Central Intelligence Agency, which conducts the bulk of drone operations in Yemen, has no drone bases on Yemeni soil but operates from Saudi Arabia and Djibouti, U.S. officials say.

They also insist that while “collateral damage” is always a risk in counterterrorism operations, they do the utmost to avoid civilian casualties.

“There must be near-certainty that no civilians will be killed or injured - the highest standard we can set,” said Alistair Baskey, a spokesman for the White House National Security Council.

Nineteen U.S. drone strikes killed 124 militants and four civilians in Yemen in 2014, according to the New America Foundation, which maintains a database of drone operations.